It makes sense if you consider subdomains as workspaces. Pieter is opening subdomain websites at wish in the context of one single big project: "Enhancing Wikidot usability". Cross Sites Includes were obvious because it was the way of easy reuse of page code.
Now a concrete example of CSL:
On a community page, we list existing modules from the official website and provide a list of links to community helpon: the listed modules:

Gerdami, yes, thanks for explaining it like this. You know I like to make lots of smaller subdomains, one per project, instead of just a single huge site with everything. Simpler and cheaper to manage, more scalable, etc. So CSIs and CSLs bring that together again.

What we learn about scaling, and the tools we make for the "Wikidot Usability Project", as Gerdami nicely describes it, are relevant to anyone doing complex, long-term work with Wikidot.